Gene detail

Detailed information of OS493_005215-T1 in Lophelia pertusa

Genomic Location: scaffold_10:4054354...4061767
NR annotation: KAJ7374862.1, Phagosome assembly factor 1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O08654	Phagosome assembly factor 1 OS=Rattus norvegicus OX=10116 GN=Phaf1 PE=2 SV=1
Q9BSU1	Phagosome assembly factor 1 OS=Homo sapiens OX=9606 GN=PHAF1 PE=1 SV=1
Q922R1	Phagosome assembly factor 1 OS=Mus musculus OX=10090 GN=Phaf1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009592 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03676 all species →	PHAF1	Phagosome assembly factor 1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039156 all species →	Family	PHAF1/Protein broad-minded	Interproscan
IPR005373 all species →	Family	Phagosome assembly factor 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13465 all species →	UPF0183 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0043001 all species →	Biological Process	Golgi to plasma membrane protein transport	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K27411	PHAF1; phagosome assembly factor 1	-	Membrane trafficking	ko04131	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_005215-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

65.1Max TPM

27.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.27	37.41
polyp at pH7 6	18	18	27.68	43.43
coral polyp · control treatment	16	16	27.66	42.93
coral polyp · oil and dispersant treatment	16	16	31.71	49.32
coral polyp · oil treatment	16	16	27.19	39.36
coral polyp · dispersant treatment	16	16	17.47	27.72
Polyp	10	10	36.31	65.07

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.99
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.49
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.93
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.82
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.76
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.18
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.81
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.75
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.49
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.43
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.62
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.59
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.58
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.95
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.44
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.01
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.54
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.36
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.14
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.23
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.03
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.96
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.65
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.55
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.58
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.20
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.38
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.32
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.84
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.62
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.29
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.23
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.64
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.30
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.32
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.15
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.31
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.75
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.16
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.46
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.81
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.73
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.40
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.57
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.71
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.25
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.36
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.99
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.64
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.63
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.45
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.02
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.91
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.97
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.71
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.44
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.97
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.97
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.16
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.72
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.85
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.47
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.92
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.04
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.97
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.75
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.14
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.23
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.82
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.94
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.17
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	65.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	64.90
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	54.67
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	44.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	41.43
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	35.51
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	18.04
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	16.51
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.16
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	8.10

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.